Protein-RNA interactions: a structural analysis

A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level

Evaluation of the Multilook Size in Polarimetric Optimization of Differential SAR Interferograms

The interferometric coherence is a measure of the correlation between two SAR images and constitutes a commonly used estimator of the phase quality. Its estimation requires a spatial average within a 2-D window, usually named as multilook. The multilook processing allows reducing noise at the expenses of a resolution loss. In this letter, we analyze the influence of the multilook size while applying a polarimetric optimization of the coherence. The same optimization algorithm has been carried out with different multilook sizes and also with the nonlocal SAR filter filter, which has the advantage of preserving the original resolution of the interferogram. Our experiments have been carried out with a single pair of quad-polarimetric RADARSAT-2 images mapping the Mount Etna's volcanic eruption of May 2008. Results obtained with this particular data set show that the coherence is increased notably with respect to conventional channels when small multilook sizes are employed, especially over low-vegetated areas. Conversely, very decorrelated areas benefit from larger multilook sizes but do not exhibit an additional improvement with the polarimetric optimization

Conformal field theories in anti-de Sitter space

In this paper we discuss the dynamics of conformal field theories on anti-de Sitter space, focussing on the special case of the N=4 supersymmetric Yang-Mills theory on AdS_4. We argue that the choice of boundary conditions, in particular for the gauge field, has a large effect on the dynamics. For example, for weak coupling, one of two natural choices of boundary conditions for the gauge field leads to a large N deconfinement phase transition as a function of the temperature, while the other does not. For boundary conditions that preserve supersymmetry, the strong coupling dynamics can be analyzed using S-duality (relevant for g_{YM} >> 1), utilizing results of Gaiotto and Witten, as well as by using the AdS/CFT correspondence (relevant for large N and large 't Hooft coupling). We argue that some very specific choices of boundary conditions lead to a simple dual gravitational description for this theory, while for most choices the gravitational dual is not known. In the cases where the gravitational dual is known, we discuss the phase structure at large 't Hooft coupling.Comment: 57 pages, 1 figure. v2: fixed typo

Polariton Condensation and Lasing

The similarities and differences between polariton condensation in microcavities and standard lasing in a semiconductor cavity structure are reviewed. The recent experiments on "photon condensation" are also reviewed.Comment: 23 pages, 6 figures; Based on the book chapter in Exciton Polaritons in Microcavities, (Springer Series in Solid State Sciences vol. 172), V. Timofeev and D. Sanvitto, eds., (Springer, 2012

Insights into GABA receptor signalling in TM3 Leydig cells

gamma-Aminobutyric acid (GABA) is an emerging signalling molecule in endocrine organs, since it is produced by endocrine cells and acts via GABA(A) receptors in a paracrine/autocrine fashion. Testicular Leydig cells are producers and targets for GABA. These cells express GABA(A) receptor subunits and in the murine Leydig cell line TM3 pharmacological activation leads to increased proliferation. The signalling pathway of GABA in these cells is not known in this study. We therefore attempted to elucidate details of GABA(A) signalling in TM3 and adult mouse Leydig cells using several experimental approaches. TM3 cells not only express GABA(A) receptor subunits, but also bind the GABA agonist {[}H-3] muscimol with a binding affinity in the range reported for other endocrine cells (K-d = 2.740 +/- 0.721 nM). However, they exhibit a low B-max value of 28.08 fmol/mg protein. Typical GABA(A) receptor-associated events, including Cl- currents, changes in resting membrane potential, intracellular Ca2+ or cAMP, were not measurable with the methods employed in TM3 cells, or, as studied in part, in primary mouse Leydig cells. GABA or GABA(A) agonist isoguvacine treatment resulted in increased or decreased levels of several mRNAs, including transcription factors (c-fos, hsf-1, egr-1) and cell cycle-associated genes (Cdk2, cyclin D1). In an attempt to verify the cDNA array results and because egr-1 was recently implied in Leydig cell development, we further studied this factor. RT-PCR and Western blotting confirmed a time-dependent regulation of egr-1 in TM3. In the postnatal testis egr-1 was seen in cytoplasmic and nuclear locations of developing Leydig cells, which bear GABA(A) receptors and correspond well to TM3 cells. Thus, GABA acts via an untypical novel signalling pathway in TM3 cells. Further details of this pathway remain to be elucidated. Copyright (c) 2005 S. Karger AG, Base

Short-term efficacy of physical interventions in osteoarthritic knee pain. A systematic review and meta-analysis of randomised placebo-controlled trials.

BACKGROUND: Treatment efficacy of physical agents in osteoarthritis of the knee (OAK) pain has been largely unknown, and this systematic review was aimed at assessing their short-term efficacies for pain relief. METHODS: Systematic review with meta-analysis of efficacy within 1-4 weeks and at follow up at 1-12 weeks after the end of treatment. RESULTS: 36 randomised placebo-controlled trials (RCTs) were identified with 2434 patients where 1391 patients received active treatment. 33 trials satisfied three or more out of five methodological criteria (Jadad scale). The patient sample had a mean age of 65.1 years and mean baseline pain of 62.9 mm on a 100 mm visual analogue scale (VAS). Within 4 weeks of the commencement of treatment manual acupuncture, static magnets and ultrasound therapies did not offer statistically significant short-term pain relief over placebo. Pulsed electromagnetic fields offered a small reduction in pain of 6.9 mm [95% CI: 2.2 to 11.6] (n = 487). Transcutaneous electrical nerve stimulation (TENS, including interferential currents), electro-acupuncture (EA) and low level laser therapy (LLLT) offered clinically relevant pain relieving effects of 18.8 mm [95% CI: 9.6 to 28.1] (n = 414), 21.9 mm [95% CI: 17.3 to 26.5] (n = 73) and 17.7 mm [95% CI: 8.1 to 27.3] (n = 343) on VAS respectively versus placebo control. In a subgroup analysis of trials with assumed optimal doses, short-term efficacy increased to 22.2 mm [95% CI: 18.1 to 26.3] for TENS, and 24.2 mm [95% CI: 17.3 to 31.3] for LLLT on VAS. Follow-up data up to 12 weeks were sparse, but positive effects seemed to persist for at least 4 weeks after the course of LLLT, EA and TENS treatment was stopped. CONCLUSION: TENS, EA and LLLT administered with optimal doses in an intensive 2-4 week treatment regimen, seem to offer clinically relevant short-term pain relief for OAK

Observation of anomalous decoherence effect in a quantum bath at room temperature

Decoherence of quantum objects is critical to modern quantum sciences and technologies. It is generally believed that stronger noises cause faster decoherence. Strikingly, recent theoretical research discovers the opposite case for spins in quantum baths. Here we report experimental observation of the anomalous decoherence effect for the electron spin-1 of a nitrogen-vacancy centre in high-purity diamond at room temperature. We demonstrate that under dynamical decoupling, the double-transition can have longer coherence time than the single-transition, even though the former couples to the nuclear spin bath as twice strongly as the latter does. The excellent agreement between the experimental and the theoretical results confirms the controllability of the weakly coupled nuclear spins in the bath, which is useful in quantum information processing and quantum metrology.Comment: 22 pages, related paper at http://arxiv.org/abs/1102.557

Information transmission in oscillatory neural activity

Periodic neural activity not locked to the stimulus or to motor responses is usually ignored. Here, we present new tools for modeling and quantifying the information transmission based on periodic neural activity that occurs with quasi-random phase relative to the stimulus. We propose a model to reproduce characteristic features of oscillatory spike trains, such as histograms of inter-spike intervals and phase locking of spikes to an oscillatory influence. The proposed model is based on an inhomogeneous Gamma process governed by a density function that is a product of the usual stimulus-dependent rate and a quasi-periodic function. Further, we present an analysis method generalizing the direct method (Rieke et al, 1999; Brenner et al, 2000) to assess the information content in such data. We demonstrate these tools on recordings from relay cells in the lateral geniculate nucleus of the cat.Comment: 18 pages, 8 figures, to appear in Biological Cybernetic

Quality of private and public ambulatory health care in low and middle income countries: systematic review of comparative studies

Paul Garner and colleagues conducted a systematic review of 80 studies to compare the quality of private versus public ambulatory health care in low- and middle-income countries